Misfires / motor stumble while accelerating 75mph+, & cold knock noise

I have a 2003 Montero Limited, 3.8L V-6, Automatic transmission. 156,000 miles.

I have had these 2 problems for a while, not sure if the symptoms are related or not. I bought it with these problems 8 months ago and have lightly driven it up to 100 miles on interstate and around town. I've put about 3,000 miles on it in the last 8 months.

On cooler mornings (about below 50 deg F) I have a knocking noise that happens for a few minutes until the engine warms up. Very infrequently it would do it on a warm morning of 80deg F, not maybe only twice all Summer, Not sure if fatigued metal or related to the next problem.

Also, at highway speeds above about 75 MPH I get a sudden vibration that feels like a missing cylinder. It happens as long as I have the accelerator on past about 75 MPH. As soon as as let off the gas pedal it stops, even if I'm above 75mph. As long as I'm under about 75 MPH it doesn't happen at usually, not enough that I recall. Sometimes over 75 MPH it's not there either. So it it doesn't always do it, but usually it does.

I have a Check Engine lite on that tells me "bank 1 burning lean". Also, my skid-traction control does not work (I bought it this way too). Sometimes the dash light comes on saying it's not on, and also that I've lost traction, and sometimes it isn't on. The traction system is not a concern to me, but if I have a weird situation happening it may have something to do with the knock and high speed stumbling.

Today I changed all the spark plugs and wires. The old ones looked fine. It ran the same for a while but then after 2 hours of highway use it began acting like it could hardly stay running and was missing very badly, like never before. I started this behavior after I had the car off for about 30 minutes while I ate lunch. It hardly wanted to start.I had to pump the gas pedal some. Almost like it was out of gas, but I had 1/8 of a tank, was on level ground, and my gas gauge has gone way below that before. I checked all the wires and connections and all was good. I drove it less than 60 MPH to get home for about 2 hours, then it stopped misfiring while doing about 35mph and began running normal again. I've driven it three times since in the same day and it hasn't done it again.

It still does the hi-speed stumble or misfiring, however, even though the really rough misfiring stopped.

What are any and all of the issues the highway speed misfiring (or something that feels like it) could be? Could a a knock-sensor or speed sensor have anything to do with the rough running? Fuel pump, clogged line, or filter issue (only does on acceleration, not coasting)? Timing? Timing belt may not have been replaced yet, along with the water pump.

What are the possibilities of the cold-morning start noises? Rod knock? Bad sensor? Pully knocking? The sound is almost like if I stuck a playing card in the spokes of a bike wheel. Steady and about that loud too. Not really loud, but noticeable for sure before it goes away (2 to 3 minutes after cold start at idle).